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Y RNA

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Y RNA
Predicted secondary structure and sequence conservation of Y_RNA
Identifiers
SymbolY_RNA
Alt. SymbolsY1; Y2; Y3; Y5
RfamRF00019
Other data
RNA typeGene
Domain(s)Eukaryota
SOSO:0000405
PDB structuresPDBe

Y RNAs are small non-coding RNAs. They are components of the Ro60 ribonucleoprotein particle[1] which is a target of autoimmune antibodies in patients with systemic lupus erythematosus.[2] They are also necessary for DNA replication through interactions with chromatin and initiation proteins.[3][4]

Structure

These small RNAs are predicted to fold into a conserved stem formed by the RNA's 3' and 5' ends and characterized by a single bulged cytosine, which are the known requirements for Ro binding.[5][6][7]

Function

A representation of the 3D structure of Y RNA bound to Ro autoantigen.[5]

Two functions have been described for Y RNAs in the literature: As a repressor of Ro60, and as an initiation factor for DNA replication. Mutant human Y RNAs lacking the conserved binding site for Ro60 protein still support DNA replication,[3] indicating that binding to Ro protein and promoting DNA replication are two separable functions of Y RNAs. Although Y RNA-derived small RNAs are similar in size to microRNAs, it has been shown that these Y RNA fragments are not involved in the microRNA pathway.[8]

Ro60 Inhibition

In its free state, Ro binds to a variety of misfolded RNAs including misfolded 5S rRNAs, and is thought to act as some sort of quality control mechanism.[9] Crystal structures of Ro complexed either with Y RNA or another RNA showed that Ro binds single-stranded 3' ends of RNAs relatively nonspecifically, whereas Y RNA binds specifically at a second site that regulates access of other RNAs.[5] In Deinococcus, free Ro has also been shown to function in 23S rRNA maturation.[10] In Deinococcus, mutants lacking Y RNA are viable, and Y RNA appears to be unstable except when complexed with Ro.[10]

DNA replication initiation

Human Y RNAs are functionally required for DNA replication.[3] Biochemical fractionation and reconstitution experiments have established a functional requirement of human Y RNAs for chromosomal DNA replication in isolated vertebrate cell nuclei in vitro[3] and specific degradation of human Y RNAs inhibits DNA replication in vitro, and in intact cells in vivo.[3] Y RNA function is thought to be mediated via interactions with chromatin and initiation proteins (including the origin recognition complex)[4]

In human pathology

Y RNAs are overexpressed in some human tumours and required for cell proliferation[11] and small, microRNA-sized breakdown products may be involved in autoimmunity and other pathological conditions.[12]

Species distribution

Presumptive Y RNA and Ro protein homologs have been found in eukaryotes and bacteria.[6][13] Humans appear to have four Y RNAs, named hY1, hY3, hY4 and hY5[13] and also a large number of pseudogenes. C. elegans has one, named CeY RNA and a large number of sbRNAs that are postulated to also be Y RNA homologues.[14][15] The radiation-resistant bacterium Deinococcus radiodurans encodes a homolog of Ro called rsr ("Ro sixty related"), and at least four small RNAs accumulate in Deinococcus under conditions where rsr expression is induced (UV irradiation); one of these RNAs appears to be a Y RNA homolog.[16]

References

  1. ^ Y RNAs: recent developments. Adam E. Hall, Carly Turnbull, Tamas Dalmay. Biomolecular Concepts. 2013 January; 4(2):103-110. doi:10.1515/bmc-2012-0050.
  2. ^ Lerner, MR (1981). "Two novel classes of small ribonucleoproteins detected by antibodies associated with lupus erythematosus". Science. 211 (4480): 400–402. doi:10.1126/science.6164096. PMID 6164096. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  3. ^ a b c d e Christov CP, Gardiner TJ, Szüts D, Krude T (2006). "Functional Requirement of Noncoding Y RNAs for Human Chromosomal DNA Replication". Mol. Cell. Biol. 26 (18): 6993–7004. doi:10.1128/MCB.01060-06. PMC 1592862. PMID 16943439.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  4. ^ a b Zhang, AT (Jun 15, 2011). "Dynamic interaction of Y RNAs with chromatin and initiation proteins during human DNA replication". Journal of cell science. 124 (Pt 12): 2058–69. PMID 21610089. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  5. ^ a b c Stein, AJ (2005). "Structural insights into RNA quality control: The Ro autoantigen binds misfolded RNAs via its central cavity". Cell. 121 (4): 529–537. doi:10.1016/j.cell.2005.03.009. PMC 1769319. PMID 15907467. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  6. ^ a b Teunissen SW, Kruithof MJ, Farris AD, Harley JB, Venrooij WJ, Pruijn GJ (2000). "Conserved features of Y RNAs: a comparison of experimentally derived secondary structures". Nucleic Acids Res. 28 (2): 610–9. doi:10.1093/nar/28.2.610. PMC 102524. PMID 10606662.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  7. ^ Green, CD (1998). "Binding of the 60-kDa Ro autoantigen to Y RNAs: evidence for recognition in the major groove of a conserved helix". RNA. 4 (7): 750–765. doi:10.1017/S1355838298971667. PMC 1369656. PMID 9671049. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  8. ^ Biogenesis of Y RNA-derived small RNAs is independent of the microRNA pathway. Francisco Esteban Nicolas, Adam E. Hall, Tibor Csorba, Carly Turnbull, Tamas Dalmay. FEBS Letters. 2012 April; 586(8):1226-1230. doi:10.1016/j.febslet.2012.03.026.
  9. ^ Reinisch, KM (2007). "Emerging themes in non-coding RNA quality control". Current Opinion in Structural Biology. 17 (2): 209–214. doi:10.1016/j.sbi.2007.03.012. PMID 17395456. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  10. ^ a b Chen X, Wurtmann EJ, Van Batavia J, Zybailov B, Washburn MP, Wolin SL (2007). "An ortholog of the Ro autoantigen functions in 23S rRNA maturation in D. radiodurans". Genes Dev. 21 (11): 1328–39. doi:10.1101/gad.1548207. PMC 1877746. PMID 17510283.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  11. ^ Christov CP, Trivier E, Krude T (March 2008). "Noncoding human Y RNAs are overexpressed in tumours and required for cell proliferation". Br. J. Cancer. 98 (5): 981–8. doi:10.1038/sj.bjc.6604254. PMC 2266855. PMID 18283318.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  12. ^ Are the Ro RNP-associated Y RNAs concealing microRNAs? Y RNA-derived miRNAs may be involved in autoimmunity. Verhagen AP, Pruijn GJ. Bioessays. 2011 Sep;33(9):674-82. doi:10.1002/bies.201100048.
  13. ^ a b Perreault J, Perreault JP, Boire G (2007). "Ro-associated Y RNAs in metazoans: evolution and diversification". Mol. Biol. Evol. 24 (8): 1678–89. doi:10.1093/molbev/msm084. PMID 17470436.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  14. ^ Van Horn, DJ (1995). "Caenorhabditis elegans embryos contain only one major species of Ro RNP". RNA. 1 (3): 293–303. PMC 1369082. PMID 7489501. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  15. ^ Boria I, Gruber AR, Tanzer A; et al. (March 2010). "Nematode sbRNAs: Homologs of Vertebrate Y RNAs". J Mol Evol. 70 (4): 346–58. doi:10.1007/s00239-010-9332-4. PMID 20349053. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link)
  16. ^ Chen, X (2000). "Ro ribonucleoproteins contribute to the resistance of Deinococcus radiodurans to ultraviolet irradiation". Genes Dev. 14 (7): 777–782. PMC 316496. PMID 10766734. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
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